Homoeologous Recombination: A Novel and Efficient System for Broadening the Genetic Variability in Wheat

Round 1

Reviewer 1 Report

The authors report the effect of Hpp-5Mg on homoeologous recombination in the absence of Ph1, where previously they published its effects in the presence of Ph1. As a result of this, they show genome-wide increases in homoeologous recombination. It is particularly interesting that they observe increased COs in proximal regions, where there is well-known difficulty in breaking linkage blocks, since COs are typically suppressed in these regions. The study is largely clear in its purpose and its findings and the findings have clear implications for downstream benefit in the generation of pre-breeding materials during wheat crop improvement. I have only minor comments that need to be addressed, parts of the writing appear a little clumsy: 

Line 34:"its 16 Gb genome is one of the largest genome among crop plants" either remove the second genome or use the plural here

Line 36: "providing more than 20% of protein and calories requirement of humans" would read better as "the protein and calorie requirement of"

Line 45: inconsistent use of landraces and land races

Line 62: Wheat repeated in sentence, could remove first mention.

Line 82: "we observed vast genome-wide increase in homoeologous" would read better as "we observed a vast genome-wide increase in homoeologous"

Table 1 would be easier to read with horizontal lines separating the rows

Line 145: "On the contrary, multiple COs and COs in proximal region between homoeologous wheat chromosomes were seldom detected in the ph1b mutant" could we quantify this? as far as I can see the COs are only in the figures to make comparisons, could we have the counts in a table or some sort of quantification in the text.

Line 249-262: The authors discuss genes controlling CO frequency in Arabidopsis, there have been similar studies conducted and genes identified in other crops and even wheat that would be relevant here, particularly with the authors focus being on wheat.

Author Response

Response to Reviewer#1

We would like to thank Reviewer#1 for his valuable suggestions and help to improve the manuscript, all of them have been incorporated in the revision. The following is a specific response to his suggestions:

Line 34:"its 16 Gb genome is one of the largest genome among crop plants" either remove the second genome or use the plural here. Changed as suggested

Line 36: "providing more than 20% of protein and calories requirement of humans" would read better as "the protein and calorie requirement of". Changed as suggested

Line 45: inconsistent use of landraces and land races. Changed as suggested

Line 62: Wheat repeated in sentence, could remove first mention. Changed as suggested

Line 82: "we observed vast genome-wide increase in homoeologous" would read better as "we observed a vast genome-wide increase in homoeologous". Changed as suggested

Table 1 would be easier to read with horizontal lines separating the rows. Changed as suggested

Line 145: "On the contrary, multiple COs and COs in proximal region between homoeologous wheat chromosomes were seldom detected in the ph1b mutant" could we quantify this? as far as I can see the COs are only in the figures to make comparisons, could we have the counts in a table or some sort of quantification in the text. We added the frequency of homoeologous recombination in ph1b genotypes as suggested.

Line 249-262: The authors discuss genes controlling CO frequency in Arabidopsis, there have been similar studies conducted and genes identified in other crops and even wheat that would be relevant here, particularly with the authors focus being on wheat. Yes of course, the genes controlling CO frequencies were reported in many crops other than Arabidopsis. However, here the discussion is restricted to wheat only. As suggested by the reviewer we discussed the effects of the HEI10 gene as reported by Jordan et al. 2018, and added this publication to the references.

Author Response File: Author Response.pdf

Reviewer 2 Report

Generally speaking, this manuscripts reads well, and contains interesting results.

There is quite some repetition in the text. As example: The authors mention in the Introduction (line 89-90) their earlier finding of 0.06% homoeologous recombination when using ph1b alone [18]. This is repeated twice in Results (line177-178 and line 187). And again in Discussion (line 240-241). I suggest to remove some redundancy.

The same holds for the first paragraph of the Discussion, describing the context of the research. This context was described already in the introduction, and repeated in the Discussion. Here again, I suggest to remove some repetition.

Please, check the spelling in Table 1 (One pair of what-Th. Intermedium translocation chromosome, involving 7BS of wheat and 7S#3L of Th. Intermedium substituting for chromosome 7B of wheat).

I hope the authors will be able to molecularly clone the Hpp-5Mg gene(s) in the near future, as that may have a huge impact on breeding in wheat and possibly also on breeding of other crops.

Author Response

Response to Reviewer#2

We would like to thank Reviewer#2 for his valuable suggestions and help to improve the manuscript, all of them have been incorporated in the revision. The following is a specific response to his suggestions:

There is quite some repetition in the text. As example: The authors mention in the Introduction (line 89-90) their earlier finding of 0.06% homoeologous recombination when using ph1b alone [18]. This is repeated twice in Results (line177-178 and line 187). And again in Discussion (line 240-241). I suggest to remove some redundancy. We have reduced this redundancy as suggested by this reviewer.

The same holds for the first paragraph of the Discussion, describing the context of the research. This context was described already in the introduction, and repeated in the Discussion. We remove some of the repetition as suggested by this reviewer.

Please, check the spelling in Table 1 (One pair of what-Th. Intermedium translocation chromosome, involving 7BS of wheat and 7S#3L of Th. Intermedium substituting for chromosome 7B of wheat). We corrected the spelling in Table 1 as suggested by this reviewer.

I hope the authors will be able to molecularly clone the Hpp-5Mg gene(s) in the near future, as that may have a huge impact on breeding in wheat and possibly also on breeding of other crops. Thank you. We realize the significance of this research and have initiated further studies aimed at analyzing the molecular mechanism of Hpp-5M^g interaction.

Author Response File: Author Response.pdf

Reviewer 3 Report

A brief summary

In this manuscript, the authors studied the effect of Hpp-5M^g on homoeologous recombination in the absence of the Ph1 locus. The authors demonstrated that Hpp-5M^g increases the probability of double crossovers in interstitial and proximal regions.

Broad comments

Introduction shows the context of the studied problem.  Materials and methods are described sufficiently. Results are well-illustrated and described in detail. It was very interesting to read the “Discussion” section, where the results were considered in the context of existing data.

Specific comments

I would suggest authors to present the crosses described in lines 178 - 183 on the scheme (in supplementary) for clarity.

Author Response

Response to Reviewer#3

We would like to thank Reviewer#1 for his valuable suggestions and help to improve the manuscript. The following is a specific response to his suggestions:

A brief summary: In this manuscript, the authors studied the effect of Hpp-5M^g on homoeologous recombination in the absence of the Ph1 locus. The authors demonstrated that Hpp-5M^g increases the probability of double crossovers in interstitial and proximal regions. Thank you.

Broad comments: Introduction shows the context of the studied problem.  Materials and methods are described sufficiently. Results are well-illustrated and described in detail. It was very interesting to read the “Discussion” section, where the results were considered in the context of existing data. Thank you.

Specific comments: I would suggest authors to present the crosses described in lines 178 - 183 on the scheme (in supplementary) for clarity. As stated clearly in the manuscript that “We crossed the ph1b mutant stock with the DS5M^g#1(5D) substitution line and then selected plants homozygous for ph1b and double monosomic for 5M^g#1 and 5D” and we strongly feel that adding an additional crossing scheme is not necessary.

Author Response File: Author Response.pdf